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Notes for PSI

df -h /media/disk/

synchronisierung auf workstation ganz links

  • grosse disk einstecken
  • evtl. mit `sudo gparted` formatieren, damit wirklich alles leer ist…
  • evtl. mit `dmesg` schauen, was lso ist, wenn nix passiert
  • `cd ~`, damit im root-verzeichnis\
  • im terminal eingeben:
rsyncdir -t 60000 --no-g --exclude-from=exclude_file.txt /sls/X02DA/data/e11126/Data10/BeamTime /media/MedionHDDrive2GO/
`-t 60000`

erhoeht die abbruchzeit, damit synchronisation nicht gestoppt wird, falls mal laenger keine daten auf Data10 geschrieben werden.

–no-g konserviert die Gruppenzugehoerigkeit, und ist seit Beamtime 2010e evtl. noetig


filelist, die die zu exkludierenden files enthaelt. in unserem fall meist


falls die rohdaten erwuenscht sind, dann `tif` aus dem exclude_file entfernen. `tif_ang` sind die resortierten 360grad-projektionen, die chris' skript mit hardlinks generiert. 'cpr' und 'fcr' kommen von der holotomography mir rajmund, rec_DMP entstehen, wenn mann falsche parameter bei der rekonstruktion eingibt.


Verzeichnis mit den Messdaten auf File-Server (einfach herauszufinden mit `pwd`)


Root-Verzeichnis der Daten auf der HD. Ohne z.B. 2009a, denn rsyncdir macht sonst `/media/disk/2009a/2009a/blabla`

am ende disk mit

eject /media/FestPlattenName


Start a Terminal and logon to the 6th node of the Cluster:

ssh e11126@x02da-cn-6

Change to the directory you need to send to the Backupserver with (for example)

cd Data3/2010a

or for example

cd Data10/2009f

Then you can generate a Textfile containing a List with Files to backup using the commands:

ls -d */tif > backupfile.txt
ls -d */rec* >> backupfile.txt
ls -d mrg/*/rec* >> backupfile.txt
ls -d mrg/*/tif* >> backupfile.txt #only if you want to backup the merged tiffs!
  • 'ls -d */tif' lists all the subdirectories containing the Projections in the directory you're in and '> backupfile.txt' writes the output of this command to a textfile with the chosen name.
  • The following commands look for other directories ('ls -d */rec*' looks for all instances of rec*-Directories, e.g. rec_8bit or rec_16bit) and appends them (using '»') to the same file. The appending is important, or else you'll loose what you've entered in the previous lines!
  • In the end we're also looking for Projections and Reconstructions in the 'mrg' subfolder, where we've written the merged Files using the widefieldscan-workflow.

To actually start the backup, you need to issue the following command (in the directory where you generated the backupfile):

bl-ftp2arch.sh -u e11126 -e david.haberthuer@psi.ch -b -P -f backupfile.txt

This starts the archiver-script for the Schittny-eAccount (-u), notifies David about success/failure (-e, email goes only to @psi-Addresses), performs the archival in the background (-b), asks for the archivFTP-Password (-P) and uses backupfile.txt as list of files to backup (-f).

If you want to monitor the progress, it's probably best if you run the command without the -b flag inside a screen-session, so you can hangup the terminal and come back.

Either follow these steps on the TOMCAT-website or:

  • Connect to slslc05.psi.ch per SSH
  • Start gFTP to have a graphical interface to the FTP-server. Start it with issuing “gftp” in the terminal.
  • login as either e11126@archivftp.psi.ch or e10277@archivftp.psi.ch. The passwords are known by the Beamline-Crew or me.
  • Browse to the directory which you want to restore.
  • Try to transfer the data. Since archivftp.psi.ch stores everything on tape, you'll probably get an error the first time. Just retry after some minutes, then everything should work like a charm.

Falls jobs manuell submitted wurden und nicht mit dem RecoManager angeschaut werden koennen, dann kann auf x02da-cons-2

cd /usr/local/cluster/DiCoClient/
java -jar DiCoClient.jar

ausgefuehrt werden. Dies started den DicoClient (Distibuted Computing Client). Mit “lj ex a” sieht mensch alle momentan ausgefuehrten, der Rest wird mit “h” erklaert.


rename R243b10_ R243b10_mrg R243b10_???.tif

or use workaround like below if “rename” does not work with more than 1000 files (seems to be the case over ssh/x-server…)

rename R243b10_0 R243b10_mrg0 R243b10_0???.tif
rename R243b10_1 R243b10_mrg1 R243b10_1???.tif
rename R243b10_2 R243b10_mrg2 R243b10_2???.tif
rename R243b10_3 R243b10_mrg3 R243b10_3???.tif
rename R243b10_4 R243b10_mrg4 R243b10_4???.tif
rdesktop pc6189 -g 1250x950 -a 16

oder mit

alias | grep CCD

rausfinden, welcher PC momentan grad zustaendig ist…

  • Start CamWare and take any picture (snap shot or movie)
  • Close CamWare
  • Start Image-Pro Plus
  • Start Camera Server FIFO
  • Camera control → Exposure, binning, etc.
  • Histogram (Histogram of image, directly linked to a particular image)
  • Flat: 40'000 - 50'000 counts.
  • Arithmetic and logical operations → divide image by flat → min. 2000 - 3000 counts in new images. If not → higher energy!!
  • Enhance - Display range: Gives histogram of current image and defines display range. May be use constantly.